New York (CNN) -- They called them the "human bucket brigade."
National Guard troops lined up in stairwells at Bellevue Hospital, carrying oil for generators up 13 flights of stairs. Superstorm Sandy had knocked out the hospital's power, and flooding had wiped out basement fuel pumps designed to power its generators.
On Wednesday, when officials at one of the country's largest hospitals decided the storm damage was too extensive to keep the facility running, those same troops helped carry patients down flights of stairs to waiting ambulances, said Alan Aviles, president of New York City Health and Hospitals Corporation.
The troops were "tireless," he said, thanking them for their efforts.
More than half of the 725 patients who were inside Bellevue when the storm hit have been transferred, Aviles told CNN on Wednesday evening. The remaining 260 patients will be evacuated by Thursday, he said.
Dozens of ambulances lined up outside the hospital to carry patients to other facilities.
Officials had hoped to keep the hospital running, Aviles said, but an investigation Wednesday revealed that the damage had been too extensive.
"The emergency generators were just not enough to keep this hospital operating for the long term," he said.
Bellevue is along the East River, just north of Manhattan's 26th Street.
Floodwaters poured into the massive hospital's 1-million-square-foot basement, Aviles said, damaging fuel pumps and water pumps that supply the complex. None of the hospital's 32 elevators is working, he said.
"It was obviously not anticipated that we would get a storm surge of this magnitude. ... We've never seen anything like this at Bellevue Hospital," Aviles said.
Officials estimate that 17 million gallons of water rushed into the hospital's basement, he said.
Most of the critically ill patients have already been evacuated, said Dr. Sanjay Gupta, CNN's chief medical correspondent, who was reporting from outside the hospital Wednesday. Gupta said moving such patients is a particularly difficult process.
"It can be very challenging ... even to transfer them within the hospital from one floor to the next. That can be a real challenge," Gupta said. "It's a very coordinated process. You always plan for the worst-case scenario. Everything from a patient's heart rate to their body temperature can change."
Gupta said evacuating the remaining patients is "likely to be more methodical, a little bit slower, perhaps even look a little more organized than over the last 24 hours."
Aviles told reporters that it was too soon to tell when the hospital would be up and running again.
"If we can get this hospital back and operating in two or three weeks, we will be doing very well," he said.
Bellevue is just a few blocks away from NYU's Langone Medical Center, where staff evacuated about 260 patients -- including newborn babies that had been in intensive care -- after the storm hit.
At times with only flashlights to illuminate the way, hospital employees carried some patients down 15 flights of stairs to ambulances ready to take them to the safety of other hospitals.
Langone didn't anticipate such heavy flooding from Sandy and chose not to evacuate all its patients before the storm.
But as the storm hit Monday night, the hospital's basement, lower floors and elevator shafts filled with 10 to 12 feet of water, and the hospital lost its power, according to Dr. Andrew Brotman, senior vice president and vice dean for clinical affairs and strategy.
"Things went downhill very, very rapidly and very unexpectedly," Brotman said. "The flooding was just unprecedented."
CNN's Elizabeth Cohen and Matt Sloane contributed to this report.